SC19: NGS for Infectious Disease Diagnostics

MONDAY, MARCH 2 | 8:00 - 11:00 AM


Next-generation sequencing technology is increasingly being used in the detection of known, uncommon, or novel pathogens with emerging clinical applications including outbreak investigation and infectious disease diagnosis. This course will discuss the applications of this technology and some of the current challenges being faced.


  • Clinical laboratory implementation of an unbiased NGS assay for pathogen detection
    • Workflow overview
  • Infrastructure needed for assay implementation
    • Control implementation for monitoring assay performance
    • Assay sensitivity across sample types (e.g., blood, bronchoalveolar lavage, cerebrospinal fluid)
    • Regulatory and quality control challenges
  • From sequence to answer: bioinformatics analysis of NGS data in infectious diseases
    • Bioinformatics pipeline (SURPI) for pathogen detection: construction and validation
    • Results reporting and interpretation for the end user
    • Challenges in interpretation (user interface, signal noise)
    • Clinical case reports of unbiased NGS for infectious disease diagnosis
  • Other applications of NGS in infectious diseases
    • 16S/18S amplicon sequencing
    • Whole-genome sequencing of bacteria and viruses
    • Microbiome analysis
    • Pathogen enrichment panels for detection and quasispecies analysis
    • Host transcriptome sequencing for biomarker identification


Chiu_CharlesCharles Chiu, MD, PhD, Associate Professor, Lab Medicine and Infectious Diseases; Director, UCSF-Abbott Viral Diagnostics and Discovery Center; Associate Director, Clinical Microbiology Laboratory, University of California, San Francisco

Dr. Charles Chiu, MD, PhD, is a Professor in Laboratory Medicine and Medicine, Infectious Diseases at the University of California, San Francisco. He is also the Director of UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC) at China Basin and Associate Director of the UCSF Clinical Microbiology Laboratory. Charles is an expert in the emerging field of clinical metagenomics, and his research is focused on the development and validation of microarray and next-generation sequencing (NGS) technologies for viral discovery and pathogen diagnostics, with over 20 patents and peer-reviewed publications on these topics. In addition, he is the principal investigator of a 5-year R01 grant from the NIH on multiplexed blood bank pathogen screening, California Discovery, UC-MEXUS, and National Research Fund for Tickborne Diseases (NRFTD) grants on the microbial epidemiology of encephalitis, diarrhea, and Lyme disease, a QB3 Rogers Family Foundation Award in translational diagnostics, and a UCSF-Abbott Viral Discovery Award. Charles is also an active practicing infectious diseases physician at UCSF. Charles has active collaborations with research groups and public health agencies worldwide, including Abbott Diagnostics, Inc., Blood Systems Research Institute, the California Department of Public Health, the United States CDC, the American Red Cross, and the Texas Biomedical Research Institute.

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